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comparison multigps.xml @ 42:8d30aeacb52a draft

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author greg
date Wed, 08 Feb 2017 12:57:32 -0500
parents 844033a58b65
children 181076e82999
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41:844033a58b65 42:8d30aeacb52a
1 <tool id="multigps" name="MultiGPS" version="0.72.0"> 1 <tool id="multigps" name="MultiGPS" version="0.73">
2 <description>analyzes collections of multi-condition ChIP-seq data</description> 2 <description>analyzes collections of multi-condition ChIP-seq data</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
7 <requirement type="package" version="0.72">multigps</requirement> 7 <requirement type="package" version="0.73">multigps</requirement>
8 </requirements> 8 </requirements>
9 <command detect_errors="aggressive"> 9 <command detect_errors="aggressive">
10 <![CDATA[ 10 <![CDATA[
11 #set output_dir = $output_html.files_path
12 mkdir -p $output_dir &&
11 multigps 13 multigps
12 ############################ 14 ############################
13 ## General options 15 ## General options
14 ############################ 16 ############################
15 --expt "$expt" 17 --expt '$expt'
16 --format "$expt.ext" 18 --format $expt.ext
17 #if $ctrl is not None: 19 #if str($ctrl) != 'None':
18 --ctrl "$ctrl" 20 --ctrl '$ctrl'
19 #end if 21 #end if
20 #if str($verbose) == 'yes': 22 #if str($verbose) == 'yes':
21 --verbose 23 --verbose
22 #end if 24 #end if
23 --threads="\${GALAXY_SLOTS:-4}" 25 --threads=\${GALAXY_SLOTS:-4}
24 --geninfo "$chromInfo" 26 --geninfo '$chromInfo'
25 ############################ 27 ############################
26 ## Advanced options 28 ## Advanced options
27 ############################ 29 ############################
28 #set aoc = $advanced_options_cond 30 #set aoc = $advanced_options_cond
29 #if str($aoc.advanced_options) == 'display': 31 #if str($aoc.advanced_options) == 'display':
31 #set gmsc = $aoc.gauss_model_smoothing_cond 33 #set gmsc = $aoc.gauss_model_smoothing_cond
32 #set rbec = $aoc.report_binding_events_cond 34 #set rbec = $aoc.report_binding_events_cond
33 #set rloc = $aoc.reads_limits_options_cond 35 #set rloc = $aoc.reads_limits_options_cond
34 #set sdc = $aoc.scale_data_cond 36 #set sdc = $aoc.scale_data_cond
35 #set umc = $aoc.use_motif_cond 37 #set umc = $aoc.use_motif_cond
36 #if str($umc.use_motif) == "yes": 38 #if str($umc.use_motif) == 'yes':
37 #set rgc = $umc.reference_genome_cond 39 #set rgc = $umc.reference_genome_cond
38 #if str($rgc.reference_genome_source) == "cached": 40 #if str($rgc.reference_genome_source) == 'cached':
39 #set seq_dir = os.path.split($rgc.reference_genome.fields.path)[0] 41 #set seq_dir = os.path.split($rgc.reference_genome.fields.path)[0]
40 #else: 42 #else:
41 ## MultiGPS requires a directory containing reference files, so symlink the history dataset. 43 ## MultiGPS requires a directory containing reference files, so symlink the history dataset.
42 #import os 44 #import os
43 #import tempfile 45 #import tempfile
44 #set seq_dir = tempfile.mkdtemp(prefix="tmp-multigps-seq-dir") 46 #set seq_dir = tempfile.mkdtemp(prefix='tmp-multigps-seq-dir')
45 #set seq_file = str($rgc.reference_genome) 47 #set seq_file = str($rgc.reference_genome)
46 #set tmp_filename = "%s.fa" % str($rgc.reference_genome.dbkey) 48 #set tmp_filename = '%s.fa' % str($rgc.reference_genome.dbkey)
47 #set tmp_seq_file = os.path.join($seq_dir, $tmp_filename) 49 #set tmp_seq_file = os.path.join($seq_dir, $tmp_filename)
48 ln -f -s $tmp_seq_file $seq_file && 50 ln -f -s $tmp_seq_file $seq_file &&
49 #end if 51 #end if
50 --seq $seq_dir 52 --seq $seq_dir
51 #end if 53 #end if
89 #end if 91 #end if
90 ############################ 92 ############################
91 ## Running MultiGPS 93 ## Running MultiGPS
92 ############################ 94 ############################
93 #if str($aoc.readdistributionfile) != 'None': 95 #if str($aoc.readdistributionfile) != 'None':
94 --d "$aoc.readdistributionfile" 96 --d '$aoc.readdistributionfile'
95 #end if 97 #end if
96 --r $aoc.maxtrainingrounds 98 --r $aoc.maxtrainingrounds
97 #if str($aoc.nomodelupdate) == 'no': 99 #if str($aoc.nomodelupdate) == 'no':
98 --nomodelupdate 100 --nomodelupdate
99 #end if 101 #end if
120 --alphascale $aoc.alphascale 122 --alphascale $aoc.alphascale
121 #if str($aoc.mlconfignotshared) == 'no': 123 #if str($aoc.mlconfignotshared) == 'no':
122 --mlconfignotshared 124 --mlconfignotshared
123 #end if 125 #end if
124 #if str($aoc.exclude) != 'None': 126 #if str($aoc.exclude) != 'None':
125 --exclude "$aoc.exclude" 127 --exclude '$aoc.exclude'
126 #end if 128 #end if
127 ############################ 129 ############################
128 ## MultiGPS priors 130 ## MultiGPS priors
129 ############################ 131 ############################
130 #if str($umc.use_motif) == 'yes': 132 #if str($umc.use_motif) == 'yes':
162 #end if 164 #end if
163 --edgerod $rbec.edgerod 165 --edgerod $rbec.edgerod
164 --diffp $rbec.diffp 166 --diffp $rbec.diffp
165 #end if 167 #end if
166 #end if 168 #end if
167 --out "$output_html.files_path" 169 --out '$output_html.files_path'
168 > "$output_html" 170 && mv $output_dir/*.html $output_html
171 && mv $output_dir/*.table $all_events_table
172 && mv $output_dir/*.counts $replicates_counts
169 ]]> 173 ]]>
170 </command> 174 </command>
171 <inputs> 175 <inputs>
172 <param name="expt" type="data" format="bam,bed,scidx" label="Run MultiGPS on"> 176 <param name="expt" type="data" format="bam,bed,scidx" label="Run MultiGPS on">
173 <validator type="unspecified_build" /> 177 <validator type="unspecified_build" />
174 </param> 178 </param>
175 <param name="ctrl" type="data" format="bam,bed,scidx" optional="True" label="Optional file containing file containing reads from a control experiment" help="Must be same forat as the input above" /> 179 <param name="ctrl" type="data" format="bam,bed,scidx" optional="True" label="Optional file containing reads from a control experiment" help="Must be same forat as the input above" />
176 <param name="verbose" type="select" label="Generate intermediate files and extra output?" help="Verbose flag"> 180 <param name="verbose" type="select" label="Generate intermediate files and extra output?" help="Verbose flag">
177 <option value="no" selected="True">No</option> 181 <option value="no" selected="True">No</option>
178 <option value="yes">Yes</option> 182 <option value="yes">Yes</option>
179 </param> 183 </param>
180 <!-- 184 <!--
409 <option value="yes">Yes</option> 413 <option value="yes">Yes</option>
410 </param> 414 </param>
411 --> 415 -->
412 </inputs> 416 </inputs>
413 <outputs> 417 <outputs>
414 <data name="output_html" format="html"/> 418 <data name="output_html" format="html" label="Results (HTML) on ${on_string}"/>
419 <data name="all_events_table" format="tabular" label="All events table on ${on_string}"/>
420 <data name="replicates_counts" format="tabular" label="Replicates counts on ${on_string}"/>
415 </outputs> 421 </outputs>
416 <tests> 422 <tests>
417 <test> 423 <test>
418 <param name="expt" value="sacCer3_1.scidx" ftype="scidx" dbkey="sacCer3"/> 424 <param name="expt" value="expt_hg19.scidx" ftype="bam" dbkey="sacCer3" />
419 <param name="binding_model_smoothing" value="no"/> 425 <param name="verbose" value="no" />
420 <param name="gaussmodelsmoothing" value="yes"/> 426 <param name="advanced_options_cond" value="hide" />
421 <param name="gausssmoothparam" value="3"/> 427 <output name="output_html" file="hg19_output_html1.html" ftype="html" lines_diff="12"/>
422 <param name="use_motif" value="yes"/> 428 <output name="all_events_table" file="hg19_all_events_table1.tabular" ftype="tabular"/>
423 <param name="reference_genome_source" value="history"/> 429 <output name="replicates_counts" file="hg19_replicates_counts1.tabular" ftype="tabular"/>
424 <param name="reference_genome" value="phiX.fasta" dbkey="phiX"/> 430 </test>
425 <param name="memenmotifs" value="3"/> 431 <test>
426 <param name="mememinw" value="6"/> 432 <param name="expt" value="expt_hg19.scidx" ftype="bam" dbkey="sacCer3" />
427 <param name="mememaxw" value="16"/> 433 <param name="ctrl" value="cntrl_hg19.scidx" ftype="bam" dbkey="sacCer3" />
428 <param name="output_process_log" value="yes"/> 434 <param name="verbose" value="no" />
429 <output name="output_process" file="output_process1.txt" ftype="txt" lines_diff="12"/> 435 <param name="advanced_options_cond" value="display" />
430 <output name="output_html" file="output_html1.html" ftype="html" lines_diff="12"/> 436 <output name="output_html" file="hg19_output_html2.html" ftype="html" lines_diff="12"/>
437 <output name="all_events_table" file="hg19_all_events_table2.tabular" ftype="tabular"/>
438 <output name="replicates_counts" file="hg19_replicates_counts2.tabular" ftype="tabular"/>
431 </test> 439 </test>
432 </tests> 440 </tests>
433 <help> 441 <help>
434 442
435 **What it does** 443 **What it does**
444 452
445 **Options** 453 **Options**
446 454
447 * **Loading data:** 455 * **Loading data:**
448 456
449 - **Optional file containing file containing reads from a control experiment** - must be same format as input experiment 457 - **Optional file containing reads from a control experiment** - must be same format as input experiment
450 - **Fixed per-base limit** - Fixed per-base limit (default: estimated from background model). 458 - **Fixed per-base limit** - Fixed per-base limit (default: estimated from background model).
451 - **Poisson threshold for filtering per base** - Look at neighboring positions to decide what the per-base limit should be. 459 - **Poisson threshold for filtering per base** - Look at neighboring positions to decide what the per-base limit should be.
452 - **Use non-unique reads** - Use non-unique reads. 460 - **Use non-unique reads** - Use non-unique reads.
453 - **Fraction of the genome that is mappable for these experiments** - Fraction of the genome that is mappable for these experiments 461 - **Fraction of the genome that is mappable for these experiments** - Fraction of the genome that is mappable for these experiments
454 - **Turn off caching of the entire set of experiments?** - Flag to turn off caching of the entire set of experiments (i.e. run slower with less memory). 462 - **Turn off caching of the entire set of experiments?** - Flag to turn off caching of the entire set of experiments (i.e. run slower with less memory).